[BioC] errors with attempted installation of package affxparser

Henrik Bengtsson hb at stat.berkeley.edu
Thu Aug 28 20:04:14 CEST 2008 

Hi,

Kasper, since you're more familar with the Makefile of affxparser,
would it be possible to output details on the version of the gcc
compiler at the beginning of the build such that it is added to the
log?

Just an idea

/Henrik


On Thu, Aug 28, 2008 at 9:35 AM, Kasper Daniel Hansen
<khansen at stat.berkeley.edu> wrote:
> Hi Mark
>
> See below for a comment, I think that (despite your attempts to work work
> around this) that you are still using GCC 4.3
>
> I will report to the main list when it works on GCC 4.3
>
> Kasper
>
> On Aug 28, 2008, at 9:21 AM, Mark Kimpel wrote:
>
>> I'm not sure what you mean by the entire compilation command, but
>> below is my install packages command, with flags for gcc-4.2 and the
>> compile output.  BTW, I just tried installing on a remote Linux
>> cluster and it installs just fine
>>
>> mkimpel at Quarry: ~> gcc --version
>> gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-10)
>>
>>
>> Here you go, please let me know if I can provide any other useful
>> information. For now, I will just use the remote cluster for what I
>> need. Will you submit a post when the problem is fixed?  Mark
>>
>>>        repos <- biocReposList()
>>>        install.packages("affxparser", repos=repos,configure.args =
>>> c('CC=/usr/bin/gcc-4.2', 'CXX=/usr/bin/g++-4.2'))
>>
>> Warning in install.packages("affxparser", repos = repos,
>> configure.args = c("CC=/usr/bin/gcc-4.2",  :
>>  argument 'lib' is missing: using
>> '/home/mkimpel/R_HOME/site-library-2.8.0'
>> trying URL
>> 'http://bioconductor.org/packages/2.3/bioc/src/contrib/affxparser_1.13.7.tar.gz'
>> Content type 'application/x-gzip' length 633900 bytes (619 Kb)
>> opened URL
>> ==================================================
>> downloaded 619 Kb
>>
>> * Installing *source* package 'affxparser' ...
>> ** libs
>> rm -f fusion_sdk/calvin_files/data/src/CDFData.o
>> fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
>> fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
>> fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o
>> fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o
>> fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o
>> fusion_sdk/calvin_files/data/src/CELData.o
>> fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o
>> fusion_sdk/calvin_files/data/src/CHPData.o
>> fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o
>> fusion_sdk/calvin_files/data/src/CHPMultiDataData.o
>> fusion_sdk/calvin_files/data/src/CHPTilingData.o
>> fusion_sdk/calvin_files/data/src/CHPQuantificationData.o
>> fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o
>> fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o
>> fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o
>> fusion_sdk/calvin_files/data/src/DataGroup.o
>> fusion_sdk/calvin_files/data/src/DataGroupHeader.o
>> fusion_sdk/calvin_files/data/src/DataSet.o
>> fusion_sdk/calvin_files/data/src/DataSetHeader.o
>> fusion_sdk/calvin_files/data/src/FileHeader.o
>> fusion_sdk/calvin_files/data/src/GenericData.o
>> fusion_sdk/calvin_files/data/src/GenericDataHeader.o
>> fusion_sdk/calvin_files/exception/src/ExceptionBase.o
>> fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
>> fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o
>> fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCDFData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
>> fusion_sdk/calvin_files/fusion/src/FusionCELData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPData.o
>> fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o
>> fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
>> fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o
>> fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o
>> fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o
>> fusion_sdk/calvin_files/parsers/src/CDFFileReader.o
>> fusion_sdk/calvin_files/parsers/src/CelFileReader.o
>> fusion_sdk/calvin_files/parsers/src/CHPFileReader.o
>> fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o
>> fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o
>> fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o
>> fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o
>> fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o
>> fusion_sdk/calvin_files/parsers/src/DataGroupReader.o
>> fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o
>> fusion_sdk/calvin_files/parsers/src/DataSetReader.o
>> fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o
>> fusion_sdk/calvin_files/parsers/src/FileInput.o
>> fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o
>> fusion_sdk/calvin_files/parsers/src/GenericFileReader.o
>> fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o
>> fusion_sdk/calvin_files/utils/src/DateTime.o
>> fusion_sdk/calvin_files/utils/src/FileUtils.o
>> fusion_sdk/calvin_files/utils/src/StringUtils.o
>> fusion_sdk/calvin_files/utils/src/checksum.o
>> fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o
>> fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o
>> fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o
>> fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/TsvFile.o
>> fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o
>> fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o
>> fusion_sdk/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o
>> R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o
>> R_affx_chp_parser.o
>> g++ -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include -imacros
>
> Here you can see that the file is being compiled with the command "g++",
> which I guess links to GCC 4.3 (just do
> # g++ --version
> on the command line)
>
> I was not aware that you can switch compilers by the config-args argument,
> and it certainly does not seem to work I would say.
>
> Kasper
>
>
>
>>
>> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src
>> -Ifusion_sdk/calvin_files/data/src
>> -Ifusion_sdk/calvin_files/exception/src
>> -Ifusion_sdk/calvin_files/fusion/src
>> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
>> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
>> -Ifusion_sdk/calvin_files/parameter/src
>> -Ifusion_sdk/calvin_files/parsers/src
>> -Ifusion_sdk/calvin_files/portability/src
>> -Ifusion_sdk/calvin_files/template/src
>> -Ifusion_sdk/calvin_files/utils/src
>> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
>> -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util
>> -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2
>> -O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o
>> fusion_sdk/calvin_files/data/src/CDFData.o
>> g++ -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include -imacros
>> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src
>> -Ifusion_sdk/calvin_files/data/src
>> -Ifusion_sdk/calvin_files/exception/src
>> -Ifusion_sdk/calvin_files/fusion/src
>> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
>> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
>> -Ifusion_sdk/calvin_files/parameter/src
>> -Ifusion_sdk/calvin_files/parsers/src
>> -Ifusion_sdk/calvin_files/portability/src
>> -Ifusion_sdk/calvin_files/template/src
>> -Ifusion_sdk/calvin_files/utils/src
>> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
>> -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util
>> -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2
>> -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp
>> -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
>> g++ -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include -imacros
>> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src
>> -Ifusion_sdk/calvin_files/data/src
>> -Ifusion_sdk/calvin_files/exception/src
>> -Ifusion_sdk/calvin_files/fusion/src
>> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
>> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
>> -Ifusion_sdk/calvin_files/parameter/src
>> -Ifusion_sdk/calvin_files/parsers/src
>> -Ifusion_sdk/calvin_files/portability/src
>> -Ifusion_sdk/calvin_files/template/src
>> -Ifusion_sdk/calvin_files/utils/src
>> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
>> -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util
>> -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2
>> -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o
>> fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
>> In file included from fusion_sdk/calvin_files/data/src/DataSet.h:25,
>>                from
>> fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:27,
>>                from
>> fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:107: error:
>> invalid type in declaration before ';' token
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:108: error:
>> expected initializer before 'WStringVectorIt'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:109: error:
>> expected initializer before 'WStringVectorConstIt'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:111: error:
>> invalid type in declaration before ';' token
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:112: error:
>> expected initializer before 'WStringListIt'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
>> 'wstring' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:113: error:
>> expected initializer before 'WStringListConstIt'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:116: error:
>> invalid type in declaration before ';' token
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:117: error:
>> expected initializer before 'StringVectorIt'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:118: error:
>> expected initializer before 'StringVectorConstIt'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:120: error:
>> invalid type in declaration before ';' token
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:121: error:
>> expected initializer before 'StringListIt'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
>> 'string' is not a member of 'std'
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
>> template argument 1 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
>> template argument 2 is invalid
>> fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h:122: error:
>> expected initializer before 'StringListConstIt'
>> In file included from
>> fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:27,
>>                from
>> fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
>> fusion_sdk/calvin_files/data/src/DataSet.h:306: error: 'void
>> affymetrix_calvin_io::DataSet::AssignValue(int32_t, WStringVector&,
>> char*&)' cannot be overloaded
>> fusion_sdk/calvin_files/data/src/DataSet.h:304: error: with 'void
>> affymetrix_calvin_io::DataSet::AssignValue(int32_t, StringVector&,
>> char*&)'
>> make: *** [fusion_sdk/calvin_files/data/src/CDFProbeInformation.o] Error 1
>> ERROR: compilation failed for package 'affxparser'
>> ** Removing '/home/mkimpel/R_HOME/site-library-2.8.0/affxparser'
>>
>> The downloaded packages are in
>>        /tmp/RtmpFcVvk1/downloaded_packages
>> Warning message:
>> In install.packages("affxparser", repos = repos, configure.args =
>> c("CC=/usr/bin/gcc-4.2",  :
>>  installation of package 'affxparser' had non-zero exit status
>>>
>>> sessionInfo()
>>
>> R version 2.8.0 Under development (unstable) (2008-08-27 r46445)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] affycoretools_1.13.3 annaffy_1.13.1       KEGG.db_2.2.3
>> [4] gcrma_2.13.1         matchprobes_1.13.1   biomaRt_1.15.1
>> [7] RCurl_0.9-4          GOstats_2.7.0        Category_2.7.4
>> [10] genefilter_1.21.3    survival_2.34-1      RBGL_1.17.2
>> [13] annotate_1.19.2      xtable_1.5-3         GO.db_2.2.3
>> [16] AnnotationDbi_1.3.9  RSQLite_0.7-0        DBI_0.2-4
>> [19] limma_2.15.11        affy_1.19.4          preprocessCore_1.3.4
>> [22] affyio_1.9.1         Biobase_2.1.7        graph_1.19.5
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.11 GSEABase_1.3.4  XML_1.96-0
>
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